More flexible command configuration

[elinscott]

This PR overhauls the koopmans.commands module in order to make the commands more customizable.

Now, the user can specify code options in the input file as follows:

    "engine": {
        "from_scratch": true,
        "commands": {
            "pw": {
                "npool": 4
            },
            "pw2wannier": {
                "pd": True
            }
        }
    },

Internally, this PR also standardizes the use of ASE_<CODE_NAME>_COMMAND environment variables (which previously were defined in different places for one calculator to the next.)

[elinscott]

Partly addresses #196 -- in the sense that it gives the user tools to overcome the errors -- but does not do so in an automated way.

[codecov]

Codecov Report

Attention: Patch coverage is 92.25806% with 24 lines in your changes missing coverage. Please review.

Project coverage is 80.69%. Comparing base (153796a) to head (69848f8).
Report is 2 commits behind head on master.

Files with missing lines	Patch %	Lines
src/koopmans/commands.py	92.07%	21 Missing ⚠️
src/koopmans/engines/localhost.py	85.71%	1 Missing ⚠️
src/koopmans/processes/_commandlinetool.py	80.00%	1 Missing ⚠️
src/koopmans/processes/bin2xml.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #245      +/-   ##
==========================================
+ Coverage   80.68%   80.69%   +0.01%     
==========================================
  Files          97       97              
  Lines        8091     8199     +108     
==========================================
+ Hits         6528     6616      +88     
- Misses       1563     1583      +20     

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